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It should be noted that Ks itself can be under selective pressures that do not act on Ka, like selection for optimal expression level based upon codon use and tRNA concentration [ 18].
Thus, phases preceding infection could also be involved in host specificity and therefore be under selective pressures.
Furthermore, we excluded 20 nucleotides upstream of the gene start codons, known to be under selective pressures due to translation initiation signals (Molina and Nimwegen 2008).
Thus, effects of somatic mutations are not misinterpreted by comparing them to the germline variants that can be under selective pressures themselves.
As mentioned before, EST-SSRs are associated with the transcribed region of the genome, thus they have a higher probability to be under selective pressures.
As a putative receptor for vesicular arbuscular endomycorrhizae (VAM) signaling, NORK might as well be under selective pressures caused by the interaction with mycorrhizal fungi.
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To check whether the loci are neutral or targeted by natural selection, the distribution of FST against the probability to be under selective pressure was simulated with BayeScan software [ 32].
Knowledge of the population genetic structure would resolve this issue by providing information on gene flow throughout the range as a point of comparison with traits that may be under selective pressure.
It has therefore been speculated that this satDNA may be under selective pressure [ 37].
Interestingly, these numbers suggest that SNPs residing within MREs are likely to be under selective pressure.
Our results further suggest MRE SNPs that modulate gene expression are likely to be under selective pressure.
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